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YouTube reply to koabarra on Ben Stein & Glenn Beck Show Intelligent Design – commented

 

(http://www.youtube.com/watch?v=293rfcliohY)

 

COMMENTS

 

In response to your supernatural comment:

 

"I believe in Christianity as I believe that the sun has risen, not only because I see it, but because by? it I see everything else."

~ C.S. Lewis

 

It is not a question of whether which one is more likely to occur. Everything in the world can be explained through either viewpoint. The question of whether he exists or not is simply a measure of what we see in the world.

 

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The most common argument is that we would obviously see complexity in the accumulation of random mutations over a long period of time.

 

However, ID does not argue that we see simply complexity. We see irreducible complexity with functionality. Most of these molecular machines would require all it's working parts to function.

 

The counter here is that the parts evolved independently of each other.

 

Problem is, that assumes that all genetic mutations are purely beneficial. There is no evidence

 

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that ANY mutation is purely beneficial. It has been repeatedly acknowledged that mutations are the LOSS of information. Evolution makes the assumption that mutation is the gaining of information. Assumptions are not science; because Science is a study of objective facts.

 

Another problem is that we have no idea what mobilizes a protein to do what it's supposed to do. How would a protein decide to do what it's NOT supposed to do, but start co-operating with another new protein from a mutation?

 

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Also, we come across the problem of never finding a single fossil of all of these millions of changes over the billions of years that would account for all these mutations to create something as complex as a human from a single-celled organism.

 

In fact, most of the "missing links" such as Lucy and Ida have also, been shown to be false. They're essentially take a tooth and reconstruct a whole skeleton around it.

 

Also, those models would be completely possible from genetic variances in the

 

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population itself. For example, if the government started to euthanize all brown eyed people, the next generation of people would have a higher percentage of people with blue or green eyes. There has not been a single mutation, but our population has (relatively) considerably changed.

 

In fact, Darwin's finches were shown to be exactly this. When the rain returned, the population's beaks also returned to it's original size.

 

This does mean that there? is an ability for populations to adapt, but

 

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this does not mean that the population will ever become? a new species.

 

That is Intelligent Design in a nutshell.

 

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REPLY

 

Hi,

 

I received your YouTube message. I will reply to your most recent set of comments that you posted on the video. I do not usually make a reply as long as this but I wanted to be thorough and perhaps thought it would be useful as a general response to the recurring arguments that occur.

 

Ok let’s talk about ID and evolution.

 

I just want to start off with your quote of C. S. Lewis. C. S. Lewis wasn’t a scientist, he was a writer and theologian. Also, he passed away before the bulk of major discoveries in biochemistry, bioinformatics and quantum gravity cosmology so he would not have been exposed to major pieces of evidence that are crucial to evolution and philosophy of theism. Why are you citing him?

 

Just a little tip. If you’re going to use ONE person’s opinion as an argument, be sure to read up on his expertise. With enormous respect to a wonderful author and an extraordinary and admirable person, I think that particular quote is very irrelevant and is merely a fancy way of expressing a subjective opinion.

 

 

First of all, let me comment on ID in general. ID, as I understand it, is the idea that certain features of the universe and living things are best explained by an intelligent cause such as an intelligent agent (http://www.ideacenter.org/contentmgr/showdetails.php/id/1136). It is based on the idea of complex-specified information (CSI), which is based on Dembski’s filter. Irreducible complexity is a subset of CSI saying that certain biological systems are too complex to have evolved from simpler, or “less complete” predecessors because all of its parts must initially be present in a suitably functioning manner (http://www.answersingenesis.org/docs/4192msc1-10-2000.asp).

 

Dembski’s filter is basically:

 

Does event E have a high probability or can it be explained by a law? If no:

Can it be explained by chance? If no:

Having rejected regularity and chance, must accept design.

 

More specifically, Dembski arbitrarily defines CSI as nonrandom information with 500 bits or more.

 

Basically this is wrong because natural selection can produce information. Dembski assumed that natural processes are incapable of producing information exceeding 500 bits. This is not so. The very early genomes were very small and contained no information. It was due to the natural selection for efficient replicators that information increased. Evolutionary mechanisms also increase information and have been operating on cells for BILLIONS of years. The filter ignores all this.

 

Another problem is that the first step asks for probabilities that are unknown, so we simply cannot perform the calculation. Also, success is badly defined and focuses on a single, specified outcome. For example, many different protein sequences can give a particular function, not just one. So it is wrong to calculate the probability of just one particular sequence.

 

See also:

http://www.newscientist.com/article/mg18725073.800-creationism-special-a-sceptics-guide-to-intelligent-design.html

 

Behe’s irreducible complexity is also simply wrong. The systems that Behe cites have all been proved to be able to have evolved naturally:

 

The “bacterial flagellum”

1.

Nat Rev Microbiol. 2006 Oct;4(10):784-90. Epub 2006 Sep 5.

From The Origin of Species to the origin of bacterial flagella.

Pallen MJ, Matzke NJ.

http://home.planet.nl/~gkorthof/pdf/Pallen_Matzke.pdf

 

This paper shows that

a) There are many different forms of the bacterial flagellum, varying in structure and mode of function and that in fact most consist of a conserved core of only about 30 proteins. This only about half of the flagellum proteins in some species, suggesting the system in these species is not even irreducibly complex.

b) Vestigial non-functional remnants of flagellar genes have been found in several bacteria.

c) Flagellar proteins have homology with each other, suggesting common evolutionary ancestry.

d) They also have homology to other non-flagellum components, further suggesting evolutionary origins.

 

2.

Trends Microbiol. 2009 Jan;17(1):1-5. Epub 2008 Dec 10.

Bacterial flagellar diversity and evolution: seek simplicity and distrust it?

Snyder LA, Loman NJ, Fütterer K, Pallen MJ.

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4V4130J-1&_user=4658158&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=4658158&md5=49d1e2cbaf2d06557aa0101f2076fca3

 

This paper shows that

a) Cut-down flagellar systems have other roles besides the flagellum.

b) Many of the proteins have functional homologs in the geneomes.

c) Not all bacteria have flagellums and that the taxonimical distribution of the genes could be a gene loss or horizontal gene transfer (HGT) scenario.

 

 

The eye

1.

Science. 2006 Sep 29;313(5795):1914-8.

Casting a genetic light on the evolution of eyes.

Fernald RD.

http://ekendil.angelfire.com/Doc/IC/Casting_a_Genetic_Light_on_the.pdf

 

This shows the evolutionary “stepping stones” for the formation of eyes.

 

2.

Curr Biol. 2005 Oct 11;15(19):R794-6.

Opsins: evolution in waiting.

Trezise AE, Collin SP.

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4H98RT1-C&_user=4658158&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=4658158&md5=77c21001da1aa35601a9660ef3cdcad7

 

Shows the evolution of the proteins that allow us to see – opsins.

 

 

Others

 

There are also examples of complicated protein complexes that have had their evolutionary history resolved. An example is complex 1:

J Mol Biol. 2005 May 13;348(4):857-70.

Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).

Gabaldón T, Rainey D, Huynen MA.

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4FPX090-4&_user=4658158&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=4658158&md5=a7cf78bb32ed161aafcca060a0ef4221

 

There are MANY examples like these. Want more? Actually, tell you what. Name a system you think is irreducibly complex.

 

 

Other ID proponents like Meyer (http://www.newscientist.com/article/dn17471-jefferson-would-not-have-supported-intelligent-design.html) make the same mistake of viewing DNA just like a code completely ignoring its evolutionary history.

 

So in conclusion, ID is not science, it is just pseudoscience. On the IDEA website they make it very clear that they THINK ID is science, accepting ANY designer, be it God, extaterrestrials, etc. However, they even admit themselves that they have a religious bias towards the God of the Bible!!! So this places ID in the realm of religious pseudoscience. What Dembski, Behe, Meyer and all those other bigots are doing is actually conjuring a “God of the gaps” argument, which is known for its cowardice and its intellectual debauchery. This is because EVEN if there wasn’t any discovered evolutionary history, it would just mean that the history of that system is unknown. As you can see, so many systems have clear or plausible evolutionary histories that it is probable the rest have just not been discovered and are simply unknown.

 

 

Let me answer your claims more specifically now.

 

You said there is no evidence that mutations have beneficial effects. Yes, there is. Most mutations are deleterious, yes, but some are beneficial. And, of course, some mutations and genetic processes can add information to the genome. I assume by beneficial mutations you mean mutations that increase your chances of survival by making you fitter to the environment you are in. Ok, here are a few. Knock yourself out.

 

1)

Circulation. 1997 Jun 17;95(12):2628-35.

Genetic variant showing a positive interaction with beta-blocking agents with a beneficial influence on lipoprotein lipase activity, HDL cholesterol, and triglyceride levels in coronary artery disease patients. The Ser447-stop substitution in the lipoprotein lipase gene. REGRESS Study Group.

Groenemeijer BE et al.

http://circ.ahajournals.org/cgi/content/full/95/12/2628

 

Mutations found in people which make them accumulate less “bad” cholesterol and therefore are less likely to suffer from circulatory disease.

 

2)

FEBS Lett. 1998 Oct 2;436(2):155-8.

Enhanced fMLP-stimulated chemotaxis in human neutrophils from individuals carrying the G protein beta3 subunit 825 T-allele.

Virchow S, Ansorge N, Rübben H, Siffert G, Siffert W.

http://www.ncbi.nlm.nih.gov/pubmed/9781669

 

A mutation in people that makes a G-protein cascade work better and therefore gives a better immune system:

 

3)

PLoS Biol. 2006 Jul;4(7):e201.

The genetic basis of thermal reaction norm evolution in lab and natural phage populations.

Knies JL, Izem R, Supler KL, Kingsolver JG, Burch CL.

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0040201

 

10 adaptive mutations found in bacteriophages (type of virus) that make them more resistant to high temperatures.

 

4)

Genetics. 1975 Apr;79(4):661-74.

Gene duplication as a mechanism of genetic adaptation in Saccharomyces cerevisiae.

Hansche PE.

http://www.genetics.org/cgi/reprint/79/4/661

 

A mutation in Yeast in the enzyme acid monophosphatase that made it better at metabolising/3-glycerophosphate.

 

5)

Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3807-12.

Genomic evolution during a 10,000-generation experiment with bacteria.

Papadopoulos D, Schneider D, Meier-Eiss J, Arber W, Lenski RE, Blot M.

http://www.pnas.org/content/96/7/3807.full

 

Mutations in a bacteria that make it grow faster and better

 

 

I can give you hundreds (literally) more if you want. Want them??? Is that proof enough for you?

 

Now, you’ve also said that “how would a protein decide to do what it's NOT supposed to do”. Well, of course it doesn’t “know” anything! Mechanisms such as gene duplication create another copy of the protein and then the proteins evolve independently and after accumulation of mutations the protein can acquire a new function. This can be things like a new active site, a new structural role or a new binding site. But the way a protein acquires new interacting partners in multimeric protein complex is often due to the self-interacting copies of a protein unit. Here, take a look at these papers – they describe the evolution of multi-protein complexes.

 

1)

Nature. 2008 Jun 26;453(7199):1262-5. Epub 2008 Jun 18.

Assembly reflects evolution of protein complexes.

Levy ED, Boeri Erba E, Robinson CV, Teichmann SA.

http://ekendil.angelfire.com/Doc/IC/Assembly_reflects_evolution_of_protein_complexes.pdf

 

2)

Genome Biol. 2007;8(4):R51.

Evolution of protein complexes by duplication of homomeric interactions.

Pereira-Leal JB, Levy ED, Kamp C, Teichmann SA.

http://genomebiology.com/2007/8/4/R51

 

3)

Nat Rev Genet. 2008 Dec;9(12):938-50.

Turning a hobby into a job: how duplicated genes find new functions.

Conant GC, Wolfe KH.

http://www.nature.com/nrg/journal/v9/n12/abs/nrg2482.html

(Abstract only)

 

 

About your comment on functionality, this is also something ID proponents don’t seem to understand. Functionality arises because of natural selection on the genome to replicate the genome more efficiently in the organism’s ecological niche. That’s all. It doesn’t show that there is a purposeful designer, it just shows adaptation of the organism for DNA replication. That is how evolution directs things and that is how it works. Therefore CSI is meaningless and cannot be used in practice.

 

 

No fossils? Lucy and Ida and the other fossils are false eh? Rubbish.

 

First of all, here is a list of transitional forms. And no, these are not just pretty pictures, they are based on REAL fossils:

http://en.wikipedia.org/wiki/List_of_transitional_fossils

Is that enough for you? How many do you need, exactly? Did you know that fossilisation of land animals is a very rare event? That is why almost all our fossils are sea-animals.

 

Ok, here is the paper for Lucy, the original paper:

Nature. 1976 Mar 25;260(5549):293-7.

Plio--Pleistocene hominid discoveries in Hadar, Ethiopia.

Johanson DC, Taieb M.

http://www.nature.com/nature/ancestor/pdf/260293.pdf

 

And for Ida:

PLoS One. 2009 May 19;4(5):e5723.

Complete primate skeleton from the Middle Eocene of Messel in Germany: morphology and paleobiology.

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, Smith BH.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005723

 

Both have detailed photographs. Are you seriously suggesting that those are all fake? Why would someone fake them? Both papers contain detailed investigation of the fossils and concluded that they are genuine transitional forms. If Lucy wasn’t genuine, why do so many scientific papers STILL go on talking about the fossil today??? For example:

J Hum Evol. 2005 Jun;48(6):593-642.

Associated cranial and forelimb remains attributed to Australopithecus afarensis from Hadar, Ethiopia.

Drapeau MS, Ward CV, Kimbel WH, Johanson DC, Rak Y.

http://ekendil.angelfire.com/Doc/fossils/Associated_cranial_and_forelimb_remains_attributed_to.pdf

 

This paper further characterises Lucy’s species, A. afarensis, as probably ancestral species to ours.

 

 

Species can’t turn into new species? Ummm...

 

Observed Instances of Speciation

http://www.talkorigins.org/faqs/faq-speciation.html

 

 

You are simply not understanding how evolution works. In your macabre example of euthanising brown-eyed people, yes, that would mimic a selection pressure, but in nature there more selection pressures, more physical barriers that separate populations and more TIME. Yes, theoretically, if you split the human population with a HUGE impenetrable wall and left them for about 3 million years, guess what? You would have 2 species. This is because in each group the mutations accumulate until the two groups are no longer genetically compatible and a sperm from one group can’t fertilise the egg of the other group to make  a baby. This is what has occured naturally for BILLIONS of years. That’s how evolution works.

 

 

You seem to be pretty ignorant about evolution in general. I cannot educate you since I have neither the time nor inclination to do so. I suggest you read this evolution primer on New Scientist:

 

http://www.newscientist.com/topic/evolution

http://www.newscientist.com/article/dn13620-evolution-24-myths-and-misconceptions.html

 

And a very good summary Nature paper:

Nature. 2009 Feb 12;457(7231):808-11.

Natural selection 150 years on.

Pagel M.

http://www.nature.com/nature/journal/v457/n7231/full/nature07889.html

(Abstract only)

 

There are also many excellent books out there.

 

 

Your arguments uncontroversially show your ignorance of biology and your probable exposure to misinformation. And see, this is why people often laugh at you guys. I learnt about A. afarensis in PRIMARY school, and this proves my point. You have been subjected, I am sorry to say, to misinformation about biology. And that’s why I am so hostile to the ideology of fundamentalist or fanatic Abrahamic monotheism. Because it is destructive on so many levels. Not only does it cause wars, it also causes retardation of human intellect. See, ALL of your arguments I have heard before by fanatic Abrahamic monotheists over and over again. And I think it’s simply because people who hold that position listen to each other and regurgitate the same  stupid arguments over and over again without taking time to actually learn about it and look at the evidence.

 

 

So here is what I suggest. Click on the links, read the papers, inform yourself using sources that are NOT religious-oriented bigotry, and then we can talk again once you have a non-biased opinion. Ideally, get a proper science degree or something if you don’t have one. I have met MANY biologists from MANY universities. Do you know how many of them reject evolution? ZERO. There is NOT a controversy about it in the scientific community.